[gmx-users] Disappear my solution

Justin A. Lemkul jalemkul at vt.edu
Fri Aug 29 00:52:14 CEST 2008

Quoting Morteza Khabiri <khabiri at greentech.cz>:

> Dear Justin
> Thanks for your prompt reply and guide.
> As you said I checked my files with gmxcheck.
> My tpr file is ok. It includes water, hexan and protein. but my edr, xtc
> and trr files have problem.
> Their faults are as follow:
> 1- for xtc: Reading frame     110 time  550.000   Fatal error: Magic
> Number Error in XTC file (read 0, should be 1995)
> 2- trr file: is empty
> 3- edr file: WARNING: there may be something wrong with energy file
> prwion.edr
> Found: step=0, nre=0, ndisre=0, nblock=0, time=0.
> Trying to skip frame expect a crash though
> But when I look at my log file everything is ok. the last part of my log
> file is:
>            Step           Time         Lambda
>         1357000     1357.00012        0.00000
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
>     3.59479e+03    5.89878e+03    2.20709e+03    1.75877e+03    2.31501e+03
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)      Potential
>     2.98386e+04    4.00479e+04   -4.96711e+03   -5.44333e+05   -4.63640e+05
>     Kinetic En.   Total Energy    Temperature Pressure (bar)
>     9.48193e+04   -3.68820e+05    3.02115e+02    4.16068e+01
> I really confused and I dont know what is the problem or on the other hand
> where is the problem. Because everything is ok till 1.3 ns after that the
> problem appear. If there is some problem it should come at the first. why
> it appear after this long time?

Probably a hardware failure, glitch in the system, or your disk may be full. 
The only problems that show up at the beginning of the simulation are those
related to improper setup.  You will have to start your run over again from the
beginning, unfortunately.  Since the .trr file is empty you cannot re-start
using tpbconv.

> I attached my mdp file also.

Please do not send files as attachments unless requested.  I generally will not
download attachments, so it is much easier to post them in the body of the

Nothing personal, I'm just cautious :)


> Thanks for your attention and guidance.
> Your sincerely,
> Morteza
> Ph.D student of Biophysics
> Laboratory of High performance computing
> Institute of Systems Biology and Ecology ASCR
> Institute of Physical Biology,
> University of South Bohemia
> Zamek 136 373 33, Nove Hrady
> Czech Republic
> Email: Khabiri at greentech.cz
> mobile: +420 773 903 109


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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